Madam, > Sir, > > Iam afraid that whether in R HTqPCR iam getting inconsistent results with > same sets of data. I have analysed same data got two different results > details of analysis and results that is given below. In both i have used > same data only difference in file.txt, in analysis1 the all normal sample > are cluster together and analysis 2 are randomly arranged. > It looks like your problem is that you don't start with a clean workspace. When you start R you should notice the line: > [Previously saved workspace restored] I.e. you ahve some old objects floating around. WHen you read in file.txt you assign it to the object "exFiles", but when you run the analysis you say "groups=files$Treatment[1:99]". The object "files" has nothing whatsover to do with your file.txt, but seems to be something left over from a previous analysis. Try starting from a clean workspace, or start out with typing rm(list=ls()). HTH \Heidi > > > Analysis 1 > > > > R version 2.11.0 (2010-04-22) > > Copyright (C) 2010 The R Foundation for Statistical Computing > > ISBN 3-900051-07-0 > > R is free software and comes with ABSOLUTELY NO WARRANTY. > > You are welcome to redistribute it under certain conditions. > > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > > Type 'contributors()' for more information and > > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > > 'help.start()' for an HTML browser interface to help. > > Type 'q()' to quit R. > > [Previously saved workspace restored] > >> library(HTqPCR) > > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > > 'openVignette()'. To cite Bioconductor, see > > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: RColorBrewer > > Loading required package: limma > >> library(limma) > >> library(RColorBrewer) > >> exPath <- "F:/HTqPCR/tlda_new_all" > >> exFiles <- read.delim(file.path(exPath, "files.txt")) > >> raw <- readCtData(files=exFiles$File[c(1:99)], path=exPath, n.features = > 48, flag = 4, feature = 6, type = 7, position = 3, Ct = 8, header = FALSE, > SDS = FALSE, n.data = 1, na.value = 40) > >> raw > > An object of class "qPCRset" > > Size: 48 features, 99 samples > > Feature types: Endogenous Control, Target > > Feature names: CCNF-Hs00171049_m1 RBL2-Hs00180562_m1 > CCND1-Hs00277039_m1 ... > > Feature classes: > > Feature categories: OK, Undetermined > > Sample names: N1 N2 N3 ... > >> path <- "F:/HTqPCR/tlda_new_all" > >> (read.delim(file.path(path, "files.txt"))) > > File Treatment > > 1 N1.txt Normal > > 2 N2.txt Normal > > 3 N3.txt Normal > > 4 N4.txt Normal > > 5 N5.txt Normal > > 6 N6.txt Normal > > 7 N7.txt Normal > > 8 N8.txt Normal > > 9 N9.txt Normal > > 10 N10.txt Normal > > 11 N11.txt Normal > > 12 N12.txt Normal > > 13 N13.txt Normal > > 14 N14.txt Normal > > 15 N15.txt Normal > > 16 N16.txt Normal > > 17 N17.txt Normal > > 18 N18.txt Normal > > 19 N19.txt Normal > > 20 N20.txt Normal > > 21 N21.txt Normal > > 22 N22.txt Normal > > 23 N23.txt Normal > > 24 N24.txt Normal > > 25 T1.txt tumor > > 26 T2.txt tumor > > 27 T3.txt tumor > > 28 T4.txt tumor > > 29 T5.txt tumor > > 30 T6.txt Normal > > 31 T7.txt Normal > > 32 T8.txt tumor > > 33 T9.txt tumor > > 34 T10.txt tumor > > 35 T11.txt tumor > > 36 T12.txt tumor > > 37 T13.txt tumor > > 38 T14.txt tumor > > 39 T15.txt tumor > > 40 T16.txt tumor > > 41 T17.txt tumor > > 42 T18.txt tumor > > 43 T19.txt tumor > > 44 T20.txt tumor > > 45 T21.txt tumor > > 46 T22.txt tumor > > 47 T23.txt tumor > > 48 T24.txt tumor > > 49 T25.txt tumor > > 50 T26.txt tumor > > 51 T27.txt tumor > > 52 T28.txt tumor > > 53 T29.txt tumor > > 54 T30.txt tumor > > 55 T31.txt tumor > > 56 T32.txt tumor > > 57 T33.txt tumor > > 58 T34.txt tumor > > 59 T35.txt tumor > > 60 T36.txt tumor > > 61 T37.txt tumor > > 62 T38.txt tumor > > 63 T39.txt tumor > > 64 T40.txt tumor > > 65 T41.txt tumor > > 66 T42.txt tumor > > 67 T43.txt tumor > > 68 T44.txt tumor > > 69 T45.txt tumor > > 70 T46.txt tumor > > 71 T47.txt tumor > > 72 T48.txt tumor > > 73 T49.txt tumor > > 74 T50.txt tumor > > 75 T51.txt tumor > > 76 T52.txt tumor > > 77 T53.txt tumor > > 78 T54.txt tumor > > 79 T55.txt tumor > > 80 T56.txt tumor > > 81 T57.txt tumor > > 82 T58.txt tumor > > 83 T59.txt tumor > > 84 T60.txt tumor > > 85 T61.txt tumor > > 86 T62.txt tumor > > 87 T63.txt tumor > > 88 T64.txt tumor > > 89 T65.txt tumor > > 90 T66.txt tumor > > 91 T67.txt tumor > > 92 T68.txt tumor > > 93 T69.txt tumor > > 94 T70.txt tumor > > 95 T71.txt tumor > > 96 T72.txt tumor > > 97 T73.txt tumor > > 98 T74.txt tumor > > 99 T75.txt tumor > >> raw.cat <- setCategory(raw, Ct.max = 38, Ct.min = 5, replicates = TRUE, > quantile = NULL, groups, flag = TRUE, flag.out = "Failed", verbose = TRUE, > plot = FALSE) > > Categories after Ct.max and Ct.min filtering: > > N1 N2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 N15 N16 N17 > N18 > N19 > > OK 48 48 47 46 48 48 48 48 48 48 48 47 48 48 48 48 43 > 48 > 48 > > Undetermined 0 0 1 2 0 0 0 0 0 0 0 1 0 0 0 0 5 > 0 > 0 > > N20 N21 N22 N23 N24 T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11 T12 > T13 > T14 > > OK 48 47 48 3 48 48 48 48 48 48 48 48 46 48 48 48 48 > 48 > 48 > > Undetermined 0 1 0 45 0 0 0 0 0 0 0 0 2 0 0 0 0 > 0 > 0 > > T15 T16 T17 T18 T19 T20 T21 T22 T23 T24 T25 T26 T27 T28 T29 > T30 > > OK 48 48 48 48 48 48 44 48 45 48 48 48 48 48 48 > 48 > > Undetermined 0 0 0 0 0 0 4 0 3 0 0 0 0 0 0 > 0 > > T31 T32 T33 T34 T35 T36 T37 T38 T39 T40 T41 T42 T43 T44 T45 > T46 > > OK 48 48 48 48 48 48 48 48 48 48 48 48 48 48 48 > 48 > > Undetermined 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > 0 > > T47 T48 T49 T50 T51 T52 T53 T54 T55 T56 T57 T58 T59 T60 T61 > T62 > > OK 47 48 48 48 48 48 48 48 48 48 48 48 48 48 48 > 48 > > Undetermined 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > 0 > > T63 T64 T65 T66 T67 T68 T69 T70 T71 T72 T73 T74 T75 > > OK 48 48 48 48 48 48 34 33 21 47 47 46 46 > > Undetermined 0 0 0 0 0 0 14 15 27 1 1 2 2 > >> q.norm <- normalizeCtDataraw.cat, norm="quantile") > >> qDE.ttest <- ttestCtData(q.norm[,1:99], groups=files$Treatment[1:99], > > + calibrator="Normal") > >> qDE.ttest[1:48,] > > genes feature.pos t.test p.value adj.p.value > > 47 TP53-Hs00153349_m1 M5 2.295891791 0.02812777 0.7125000 > > 31 CDKN2A-Hs00233365_m1 N9 -2.082255233 0.04380924 0.7125000 > > 2 ATM-Hs00175892_m1 N23 1.937805071 0.06000455 0.7125000 > > 4 BCL2-Hs00608023_m1 N24 1.770657925 0.08396548 0.7125000 > > 24 CDK5-Hs00358991_g1 N5 -1.666016360 0.10350732 0.7125000 > > 20 CDC25C-Hs00156411_m1 M12 1.630183670 0.10933804 0.7125000 > > 27 CDK8-Hs00176209_m1 M14 -1.546067079 0.12925207 0.7125000 > > 46 TGFA-Hs00608187_m1 N22 -1.547216622 0.12962975 0.7125000 > > 36 E2F1-Hs00153451_m1 N13 1.496405692 0.14153371 0.7125000 > > 3 ATR-Hs00169878_m1 N16 1.424482218 0.16073293 0.7125000 > > 33 CDKN2C-Hs00176227_m1 N15 1.329395172 0.19193228 0.7125000 > > 1 18S-Hs99999901_s1 M11 1.330427353 0.19295059 0.7125000 > > 14 CCNF-Hs00171049_m1 M1 -1.264650510 0.21288347 0.7125000 > > 25 CDK6-Hs00608037_m1 M13 -1.260494621 0.21591150 0.7125000 > > 29 CDKN1B-Hs00153277_m1 M20 1.197283433 0.23807788 0.7125000 > > 9 CCND1-Hs00277039_m1 M3 1.186232786 0.24153101 0.7125000 > > 16 CCNH-Hs00236923_m1 M18 1.159827899 0.25234377 0.7125000 > > 42 PIN1-Hs00749260_s1 M7 -1.017033208 0.31677086 0.7312508 > > 44 RBL1-Hs00765707_m1 N6 -0.990603791 0.32746372 0.7312508 > > 35 CHEK1-Hs00176236_m1 M4 -0.984312292 0.32974562 0.7312508 > > 22 CDK2-Hs00608082_m1 N7 0.921231845 0.36229801 0.7312508 > > 19 CDC20-Hs00415851_g1 N20 -0.891251276 0.37816127 0.7312508 > > 30 CDKN1C-Hs00175938_m1 N17 0.885721819 0.38133275 0.7312508 > > 23 CDK4-Hs00364847_m1 M10 0.880593383 0.38332999 0.7312508 > > 38 EGFR-Hs00193306_m1 M6 -0.861446299 0.39248804 0.7312508 > > 48 TP53BP2-Hs00610488_m1 M17 -0.859232889 0.39609417 0.7312508 > > 26 CDK7-Hs00757090_g1 N8 -0.793062156 0.43214696 0.7682613 > > 8 CCNC-Hs00193177_m1 M8 -0.748176629 0.46024346 0.7780245 > > 39 GADD45A-Hs00169255_m1 N4 0.730384641 0.47005649 0.7780245 > > 12 CCNE1-Hs00233356_m1 N11 -0.661190280 0.51247743 0.8199639 > > 40 MDM2-Hs00242813_m1 N14 0.523011580 0.60315433 0.9162412 > > 32 CDKN2B-Hs00793225_m1 M16 -0.511063425 0.61082746 0.9162412 > > 18 CDC2-Hs00364293_m1 N21 0.424545098 0.67372768 0.9398924 > > 6 CCNB1-Hs00259126_m1 M23 -0.397648195 0.69294867 0.9398924 > > 43 RB1-Hs00153108_m1 M24 -0.356106465 0.72438495 0.9398924 > > 21 CDC34-Hs00362082_m1 M9 -0.347115072 0.73067318 0.9398924 > > 7 CCNB2-Hs00270424_m1 N19 0.343158811 0.73340270 0.9398924 > > 45 RBL2-Hs00180562_m1 M2 0.301231001 0.76499875 0.9398924 > > 37 E2F2-Hs00231667_m1 N12 0.264437309 0.79257682 0.9398924 > > 17 CCNK-Hs00395018_m1 N2 0.250846802 0.80298088 0.9398924 > > 41 MKI67-Hs00606991_m1 M19 -0.221244374 0.82592897 0.9398924 > > 13 CCNE2-Hs00180319_m1 N18 0.207823187 0.83649945 0.9398924 > > 34 CDKN2D-Hs00176481_m1 N10 -0.200743474 0.84198691 0.9398924 > > 11 CCND3-Hs00426901_m1 M15 -0.136550193 0.89195280 0.9511576 > > 15 CCNG2-Hs00171119_m1 M21 0.124235792 0.90172251 0.9511576 > > 28 CDKN1A-Hs00355782_m1 N3 0.111822460 0.91152601 0.9511576 > > 5 CCNA1-Hs00171105_m1 M22 -0.051450616 0.95924075 0.9796501 > > 10 CCND2-Hs00277041_m1 N1 0.001033206 0.99918012 0.9991801 > > ddCt FC meanCalibrator meanTarget categoryTarget > > 47 -0.5771835615 1.4919338 28.29557 27.71839 Undetermined > > 31 1.2149986166 0.4307735 26.10425 27.31925 Undetermined > > 2 -0.4342070891 1.3511680 29.73063 29.29643 Undetermined > > 4 -0.7067142098 1.6320828 30.29411 29.58740 Undetermined > > 24 0.2932291238 0.8160734 27.90855 28.20178 Undetermined > > 20 -0.3931802780 1.3132852 32.55413 32.16095 Undetermined > > 27 0.2315856136 0.8516983 27.81600 28.04759 Undetermined > > 46 0.5136423509 0.7004518 26.83748 27.35112 Undetermined > > 36 -0.3443487024 1.2695777 29.15093 28.80658 Undetermined > > 3 -0.2234603706 1.1675306 28.68034 28.45687 Undetermined > > 33 -0.4275325781 1.3449314 30.19377 29.76624 Undetermined > > 1 -1.5299479008 2.8877541 11.84900 10.31905 OK > > 14 NA NA NA 27.57528 Undetermined > > 25 0.2203066750 0.8583829 26.65416 26.87446 Undetermined > > 29 -0.2577058577 1.1955760 26.47668 26.21897 Undetermined > > 9 -0.3473309551 1.2722048 26.85627 26.50894 Undetermined > > 16 -0.1645688561 1.1208311 28.09055 27.92598 Undetermined > > 42 NA NA 22.82325 NA OK > > 44 0.1898566073 0.8766929 28.86255 29.05241 Undetermined > > 35 0.1946000847 0.8738151 28.21858 28.41318 Undetermined > > 22 -0.1650715778 1.1212217 29.11399 28.94892 Undetermined > > 19 0.3223268749 0.7997789 26.74567 27.06800 Undetermined > > 30 -0.5765941675 1.4913245 28.00179 27.42520 Undetermined > > 23 -0.3528688765 1.2770977 25.44603 25.09316 Undetermined > > 38 0.1870928877 0.8783739 26.18928 26.37638 Undetermined > > 48 0.1326862796 0.9121315 27.71044 27.84313 Undetermined > > 26 0.1239877900 0.9176476 28.00722 28.13121 Undetermined > > 8 0.1290736586 0.9144184 26.98845 27.11752 Undetermined > > 39 -0.1728404506 1.1272757 28.36314 28.19030 Undetermined > > 12 0.1829117466 0.8809233 29.45615 29.63906 Undetermined > > 40 -0.1034057465 1.0743066 26.39775 26.29434 Undetermined > > 32 NA NA 27.81330 NA Undetermined > > 18 -0.0869243673 1.0621035 28.34943 28.26251 Undetermined > > 6 0.0906105280 0.9391252 28.06654 28.15715 Undetermined > > 43 0.0968366238 0.9350811 27.29783 27.39467 Undetermined > > 21 0.0659027358 0.9553473 26.67284 26.73874 Undetermined > > 7 -0.1037258208 1.0745449 27.63123 27.52750 Undetermined > > 45 -0.0574024676 1.0405905 27.51019 27.45279 Undetermined > > 37 -0.0947104615 1.0678511 28.89725 28.80254 Undetermined > > 17 -0.0259664431 1.0181615 26.96487 26.93890 Undetermined > > 41 0.0688651399 0.9533877 27.51280 27.58166 Undetermined > > 13 -0.0416421111 1.0292847 30.18775 30.14610 Undetermined > > 34 0.0403632814 0.9724101 28.51461 28.55498 Undetermined > > 11 0.0247566698 0.9829864 26.77960 26.80436 Undetermined > > 15 -0.0188040565 1.0131193 27.74717 27.72837 Undetermined > > 28 -0.0586069931 1.0414597 22.90229 22.84369 Undetermined > > 5 NA NA NA NA Undetermined > > 10 -0.0002114316 1.0001466 26.40150 26.40128 Undetermined > > categoryCalibrator > > 47 OK > > 31 OK > > 2 OK > > 4 Undetermined > > 24 OK > > 20 Undetermined > > 27 OK > > 46 OK > > 36 OK > > 3 OK > > 33 OK > > 1 OK > > 14 OK > > 25 OK > > 29 OK > > 9 OK > > 16 OK > > 42 OK > > 44 OK > > 35 OK > > 22 OK > > 19 OK > > 30 OK > > 23 OK > > 38 OK > > 48 OK > > 26 OK > > 8 OK > > 39 OK > > 12 OK > > 40 OK > > 32 OK > > 18 OK > > 6 OK > > 43 Undetermined > > 21 OK > > 7 OK > > 45 OK > > 37 OK > > 17 OK > > 41 OK > > 13 OK > > 34 OK > > 11 OK > > 15 OK > > 28 OK > > 5 Undetermined > > 10 OK > >> write.table(qDE.ttest, file="test20.xls", sep="\t", quote=FALSE, > row.names=FALSE) > >> sessionInfo() > > R version 2.11.0 (2010-04-22) > > x86_64-pc-mingw32 > > locale: > > [1] LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252 > > [3] LC_MONETARY=English_India.1252 LC_NUMERIC=C > > [5] LC_TIME=English_India.1252 > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > > [1] HTqPCR_1.2.0 limma_3.4.3 RColorBrewer_1.0-2 Biobase_2.8.0 > > > loaded via a namespace (and not attached): > > [1] affy_1.26.1 affyio_1.16.0 gdata_2.8.0 > > [4] gplots_2.8.0 gtools_2.6.2 preprocessCore_1.10.0 > > > > > > > > > > Analysis 2 > > > > R version 2.11.0 (2010-04-22) > > Copyright (C) 2010 The R Foundation for Statistical Computing > > ISBN 3-900051-07-0 > > > > R is free software and comes with ABSOLUTELY NO WARRANTY. > > You are welcome to redistribute it under certain conditions. > > Type 'license()' or 'licence()' for distribution details. > > > > Natural language support but running in an English locale > > > > R is a collaborative project with many contributors. > > Type 'contributors()' for more information and > > 'citation()' on how to cite R or R packages in publications. > > > > Type 'demo()' for some demos, 'help()' for on-line help, or > > 'help.start()' for an HTML browser interface to help. > > Type 'q()' to quit R. > > > > [Previously saved workspace restored] > > > >> library(HTqPCR) > > Loading required package: Biobase > > > > Welcome to Bioconductor > > > > Vignettes contain introductory material. To view, type > > 'openVignette()'. To cite Bioconductor, see > > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > > > Loading required package: RColorBrewer > > Loading required package: limma > >> library(limma) > >> library(RColorBrewer) > >> exPath <- "F:/HTqPCR/tlda_new_all" > >> exFiles <- read.delim(file.path(exPath, "files.txt")) > >> raw <- readCtData(files=exFiles$File[c(1:99)], path=exPath, n.features = > 48, flag = 4, feature = 6, type = 7, position = 3, Ct = 8, header = FALSE, > SDS = FALSE, n.data = 1, na.value = 40) > >> raw > > An object of class "qPCRset" > > Size: 48 features, 99 samples > > Feature types: Endogenous Control, Target > > Feature names: CCNF-Hs00171049_m1 RBL2-Hs00180562_m1 > CCND1-Hs00277039_m1 ... > > Feature classes: > > Feature categories: OK, Undetermined > > Sample names: T1 T2 T3 ... > >> path <- "F:/HTqPCR/tlda_new_all" > >> (read.delim(file.path(path, "files.txt"))) > > File Treatment > > 1 T1.txt Tumor > > 2 T2.txt Tumor > > 3 T3.txt Tumor > > 4 T4.txt Tumor > > 5 T5.txt Tumor > > 6 N1.txt Normal > > 7 T6.txt Normal > > 8 T7.txt Normal > > 9 T8.txt Tumor > > 10 T9.txt Tumor > > 11 T10.txt Tumor > > 12 T11.txt Tumor > > 13 N2.txt Normal > > 14 T12.txt Tumor > > 15 T13.txt Tumor > > 16 N3.txt Normal > > 17 T14.txt Tumor > > 18 N4.txt Normal > > 19 T15.txt Tumor > > 20 T16.txt Tumor > > 21 T17.txt Tumor > > 22 N5.txt Normal > > 23 T18.txt Tumor > > 24 N6.txt Normal > > 25 N7.txt Normal > > 26 T19.txt Tumor > > 27 T20.txt Tumor > > 28 N8.txt Normal > > 29 T21.txt Tumor > > 30 T22.txt Tumor > > 31 T23.txt Tumor > > 32 N9.txt Normal > > 33 T24.txt Tumor > > 34 T25.txt Tumor > > 35 T26.txt Tumor > > 36 T27.txt Tumor > > 37 T28.txt Tumor > > 38 T29.txt Tumor > > 39 T30.txt Tumor > > 40 T31.txt Tumor > > 41 T32.txt Tumor > > 42 T33.txt Tumor > > 43 T34.txt Tumor > > 44 T35.txt Tumor > > 45 T36.txt Tumor > > 46 T37.txt Tumor > > 47 T38.txt Tumor > > 48 N10.txt Normal > > 49 T39.txt Tumor > > 50 T40.txt Tumor > > 51 T41.txt Tumor > > 52 N11.txt Normal > > 53 T42.txt Tumor > > 54 T43.txt Tumor > > 55 T44.txt Tumor > > 56 T45.txt Tumor > > 57 T46.txt Tumor > > 58 T47.txt Tumor > > 59 T48.txt Tumor > > 60 T49.txt Tumor > > 61 N12.txt Normal > > 62 T50.txt Tumor > > 63 T51.txt Tumor > > 64 N13.txt Normal > > 65 T52.txt Tumor > > 66 T53.txt Tumor > > 67 T54.txt Tumor > > 68 N14.txt Normal > > 69 T55.txt Tumor > > 70 N15.txt Normal > > 71 T56.txt Tumor > > 72 N16.txt Normal > > 73 T57.txt Tumor > > 74 T58.txt Tumor > > 75 T59.txt Tumor > > 76 N17.txt Normal > > 77 T60.txt Tumor > > 78 N18.txt Normal > > 79 T61.txt Tumor > > 80 T62.txt Tumor > > 81 T63.txt Tumor > > 82 T64.txt Tumor > > 83 T65.txt Tumor > > 84 N19.txt Normal > > 85 T66.txt Tumor > > 86 N20.txt Normal > > 87 T67.txt Tumor > > 88 N21.txt Normal > > 89 T68.txt Tumor > > 90 N22.txt Normal > > 91 T69.txt Tumor > > 92 N23.txt Normal > > 93 T70.txt Tumor > > 94 T71.txt Tumor > > 95 T72.txt Tumor > > 96 T73.txt Tumor > > 97 T74.txt Tumor > > 98 T75.txt Tumor > > 99 N24.txt Normal > >> raw.cat <- setCategory(raw, Ct.max = 38, Ct.min = 5, replicates = TRUE, > quantile = NULL, groups, flag = TRUE, flag.out = "Failed", verbose = TRUE, > plot = FALSE) > > Categories after Ct.max and Ct.min filtering: > > T1 T2 T3 T4 T5 N1 T6 T7 T8 T9 T10 T11 N2 T12 T13 N3 T14 N4 > T15 > T16 > > OK 48 48 48 48 48 48 48 48 46 48 48 48 48 48 48 47 48 46 > 48 > 48 > > Undetermined 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 1 0 2 > 0 > 0 > > T17 N5 T18 N6 N7 T19 T20 N8 T21 T22 T23 N9 T24 T25 T26 T27 > T28 > T29 > > OK 48 48 48 48 48 48 48 48 44 48 45 48 48 48 48 48 > 48 > 48 > > Undetermined 0 0 0 0 0 0 0 0 4 0 3 0 0 0 0 0 > 0 > 0 > > T30 T31 T32 T33 T34 T35 T36 T37 T38 N10 T39 T40 T41 N11 T42 > T43 > > OK 48 48 48 48 48 48 48 48 48 48 48 48 48 48 48 > 48 > > Undetermined 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > 0 > > T44 T45 T46 T47 T48 T49 N12 T50 T51 N13 T52 T53 T54 N14 T55 > N15 > > OK 48 48 48 47 48 48 47 48 48 48 48 48 48 48 48 > 48 > > Undetermined 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 > 0 > > T56 N16 T57 T58 T59 N17 T60 N18 T61 T62 T63 T64 T65 N19 T66 > N20 > > OK 48 48 48 48 48 43 48 48 48 48 48 48 48 48 48 > 48 > > Undetermined 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 > 0 > > T67 N21 T68 N22 T69 N23 T70 T71 T72 T73 T74 T75 N24 > > OK 48 47 48 48 34 3 33 21 47 47 46 46 48 > > Undetermined 0 1 0 0 14 45 15 27 1 1 2 2 0 > >> q.norm <- normalizeCtDataraw.cat, norm="quantile") > >> qDE.ttest <- ttestCtData(q.norm[,1:99], groups=files$Treatment[1:99], > > + calibrator="Normal") > >> qDE.ttest[1:48,] > > genes feature.pos t.test p.value adj.p.value > > 6 CCNB1-Hs00259126_m1 I23 6.20160729 7.048712e-08 3.383382e-06 > > 35 CHEK1-Hs00176236_m1 I4 5.48408184 2.514510e-06 6.034823e-05 > > 46 TGFA-Hs00608187_m1 J22 5.21382975 4.743489e-06 7.589583e-05 > > 4 BCL2-Hs00608023_m1 J24 -4.65741536 2.384561e-05 2.861473e-04 > > 47 TP53-Hs00153349_m1 I5 -4.34020615 5.356469e-05 5.142210e-04 > > 25 CDK6-Hs00608037_m1 I13 4.15810415 9.191490e-05 7.092438e-04 > > 33 CDKN2C-Hs00176227_m1 J15 -4.24782850 1.034314e-04 7.092438e-04 > > 16 CCNH-Hs00236923_m1 I18 -3.88720229 2.996959e-04 1.798176e-03 > > 9 CCND1-Hs00277039_m1 I3 -3.90103610 3.929839e-04 2.095914e-03 > > 18 CDC2-Hs00364293_m1 J21 3.68357070 6.744105e-04 3.237170e-03 > > 12 CCNE1-Hs00233356_m1 J11 3.61548837 8.202665e-04 3.579345e-03 > > 29 CDKN1B-Hs00153277_m1 I20 -3.58651890 9.334087e-04 3.733635e-03 > > 30 CDKN1C-Hs00175938_m1 J17 -3.46267415 1.165720e-03 4.304198e-03 > > 45 RBL2-Hs00180562_m1 I2 -3.33108991 1.570514e-03 5.384621e-03 > > 39 GADD45A-Hs00169255_m1 J4 -3.27745675 2.135930e-03 6.834977e-03 > > 41 MKI67-Hs00606991_m1 I19 3.17081035 2.819846e-03 8.459537e-03 > > 7 CCNB2-Hs00270424_m1 J19 2.98768802 5.280899e-03 1.491077e-02 > > 27 CDK8-Hs00176209_m1 I14 -2.78622102 8.490709e-03 2.264189e-02 > > 10 CCND2-Hs00277041_m1 J1 2.52336007 1.446031e-02 3.653131e-02 > > 2 ATM-Hs00175892_m1 J23 -2.49985908 1.640807e-02 3.937937e-02 > > 19 CDC20-Hs00415851_g1 J20 2.42245447 2.076797e-02 4.591003e-02 > > 14 CCNF-Hs00171049_m1 I1 2.42086969 2.104210e-02 4.591003e-02 > > 3 ATR-Hs00169878_m1 J16 -2.32874362 2.407737e-02 5.024842e-02 > > 34 CDKN2D-Hs00176481_m1 J10 -2.19062609 3.304834e-02 6.609668e-02 > > 17 CCNK-Hs00395018_m1 J2 -2.18165397 3.542196e-02 6.801016e-02 > > 48 TP53BP2-Hs00610488_m1 I17 -1.92606707 6.038405e-02 1.114783e-01 > > 13 CCNE2-Hs00180319_m1 J18 1.85171704 7.355627e-02 1.307667e-01 > > 5 CCNA1-Hs00171105_m1 I22 1.68689949 9.901674e-02 1.697430e-01 > > 31 CDKN2A-Hs00233365_m1 J9 1.53778250 1.301844e-01 2.091751e-01 > > 40 MDM2-Hs00242813_m1 J14 -1.54259099 1.307344e-01 2.091751e-01 > > 21 CDC34-Hs00362082_m1 I9 -1.49644686 1.444121e-01 2.236059e-01 > > 26 CDK7-Hs00757090_g1 J8 -1.46834115 1.491629e-01 2.237444e-01 > > 37 E2F2-Hs00231667_m1 J12 -1.34939756 1.841182e-01 2.678083e-01 > > 1 18S-Hs99999901_s1 I11 -1.22892059 2.246587e-01 3.171652e-01 > > 11 CCND3-Hs00426901_m1 I15 1.19278926 2.393266e-01 3.282194e-01 > > 44 RBL1-Hs00765707_m1 J6 -1.09090637 2.849470e-01 3.799293e-01 > > 43 RB1-Hs00153108_m1 I24 0.94267649 3.498142e-01 4.538131e-01 > > 32 CDKN2B-Hs00793225_m1 I16 0.92879772 3.593685e-01 4.539392e-01 > > 42 PIN1-Hs00749260_s1 I7 0.82347162 4.139756e-01 5.095084e-01 > > 36 E2F1-Hs00153451_m1 J13 0.49857447 6.211263e-01 7.349228e-01 > > 22 CDK2-Hs00608082_m1 J7 0.48826165 6.277465e-01 7.349228e-01 > > 23 CDK4-Hs00364847_m1 I10 -0.31376143 7.554674e-01 8.614452e-01 > > 15 CCNG2-Hs00171119_m1 I21 0.29249852 7.717113e-01 8.614452e-01 > > 28 CDKN1A-Hs00355782_m1 J3 -0.25546174 7.999394e-01 8.634675e-01 > > 24 CDK5-Hs00358991_g1 J5 0.24250526 8.095008e-01 8.634675e-01 > > 38 EGFR-Hs00193306_m1 I6 -0.20599698 8.373903e-01 8.737986e-01 > > 8 CCNC-Hs00193177_m1 I8 -0.16344607 8.712155e-01 8.897520e-01 > > 20 CDC25C-Hs00156411_m1 I12 -0.06573621 9.479508e-01 9.479508e-01 > > ddCt FC meanCalibrator meanTarget categoryTarget > > 6 -1.07648601 2.1088932 28.95070 27.87422 Undetermined > > 35 -1.06811289 2.0966890 29.17518 28.10707 Undetermined > > 46 -1.49585130 2.8203052 28.35982 26.86397 Undetermined > > 4 1.58320841 0.3337389 28.55932 30.14253 Undetermined > > 47 0.76174256 0.5897835 27.28123 28.04298 OK > > 25 -0.49744752 1.4117137 27.19791 26.70046 Undetermined > > 33 1.12458260 0.4586347 29.01792 30.14251 Undetermined > > 16 0.49405366 0.7100273 27.59160 28.08565 OK > > 9 1.21875736 0.4296526 25.66984 26.88860 OK > > 18 -0.65334131 1.5728066 28.77853 28.12519 Undetermined > > 12 -0.90777004 1.8761433 30.28242 29.37465 Undetermined > > 29 0.75834453 0.5911743 25.70694 26.46529 OK > > 30 1.93646182 0.2612564 26.09796 28.03443 OK > > 45 0.48721017 0.7134033 27.09761 27.58482 OK > > 39 0.66461173 0.6308585 27.72870 28.39331 Undetermined > > 41 -0.96027455 1.9456801 28.29245 27.33217 Undetermined > > 7 -0.93770737 1.9154819 28.26303 27.32532 Undetermined > > 27 0.45887090 0.7275554 27.64381 28.10269 Undetermined > > 10 -0.45803273 1.3736674 26.74833 26.29030 OK > > 2 0.52684258 0.6940721 29.00257 29.52941 Undetermined > > 19 -0.92813803 1.9028186 27.69299 26.76485 Undetermined > > 14 NA NA NA 27.35398 Undetermined > > 3 0.35954577 0.7794099 28.23866 28.59821 Undetermined > > 34 0.36531112 0.7763014 28.26844 28.63375 OK > > 17 0.25381909 0.8386733 26.75291 27.00673 Undetermined > > 48 0.25068667 0.8404963 27.62105 27.87173 Undetermined > > 13 -0.41472318 1.3330429 30.47038 30.05566 Undetermined > > 5 NA NA NA NA Undetermined > > 31 -0.79234046 1.7318818 27.62496 26.83262 Undetermined > > 40 0.34543993 0.7870679 26.05771 26.40315 Undetermined > > 21 0.29287706 0.8162726 26.50089 26.79377 OK > > 26 0.22446161 0.8559144 27.93111 28.15557 Undetermined > > 37 0.50080229 0.7067137 28.44610 28.94690 Undetermined > > 1 1.04957648 0.4831100 9.89481 10.94439 OK > > 11 -0.22504377 1.1688127 26.96884 26.74380 Undetermined > > 44 0.29970271 0.8124198 28.77934 29.07904 Undetermined > > 43 -0.16428205 1.1206083 27.49565 27.33137 Undetermined > > 32 NA NA 28.34727 NA Undetermined > > 42 NA NA 25.12208 NA OK > > 36 -0.13237465 1.0960964 28.99034 28.85797 Undetermined > > 22 -0.08383105 1.0598287 29.05245 28.96862 Undetermined > > 23 0.13964048 0.9077453 25.07292 25.21256 OK > > 15 -0.05127164 1.0361778 27.77177 27.72050 Undetermined > > 28 0.15128081 0.9004507 22.74329 22.89457 OK > > 24 -0.04078961 1.0286767 28.16160 28.12081 Undetermined > > 38 0.04184529 0.9714117 26.29932 26.34117 Undetermined > > 8 0.02687468 0.9815443 27.06587 27.09275 OK > > 20 0.01922018 0.9867659 32.24171 32.26093 Undetermined > > categoryCalibrator > > 6 Undetermined > > 35 Undetermined > > 46 Undetermined > > 4 Undetermined > > 47 Undetermined > > 25 Undetermined > > 33 Undetermined > > 16 Undetermined > > 9 Undetermined > > 18 Undetermined > > 12 Undetermined > > 29 Undetermined > > 30 Undetermined > > 45 Undetermined > > 39 Undetermined > > 41 Undetermined > > 7 Undetermined > > 27 Undetermined > > 10 Undetermined > > 2 Undetermined > > 19 Undetermined > > 14 Undetermined > > 3 Undetermined > > 34 Undetermined > > 17 Undetermined > > 48 Undetermined > > 13 Undetermined > > 5 Undetermined > > 31 Undetermined > > 40 Undetermined > > 21 Undetermined > > 26 Undetermined > > 37 Undetermined > > 1 OK > > 11 Undetermined > > 44 Undetermined > > 43 Undetermined > > 32 Undetermined > > 42 OK > > 36 Undetermined > > 22 Undetermined > > 23 Undetermined > > 15 Undetermined > > 28 Undetermined > > 24 Undetermined > > 38 Undetermined > > 8 Undetermined > > 20 Undetermined > >> sessionInfo() > > R version 2.11.0 (2010-04-22) > > x86_64-pc-mingw32 > > > > locale: > > [1] LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252 > > [3] LC_MONETARY=English_India.1252 LC_NUMERIC=C > > [5] LC_TIME=English_India.1252 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] HTqPCR_1.2.0 limma_3.4.3 RColorBrewer_1.0-2 Biobase_2.8.0 > > > > > loaded via a namespace (and not attached): > > [1] affy_1.26.1 affyio_1.16.0 gdata_2.8.0 > > [4] gplots_2.8.0 gtools_2.6.2 preprocessCore_1.10.0 > >> > > > -- > Deepak Roshan V G > Laboratory Of Cell Cycle Regulation & Molecular Oncology > Division of Cancer Research > Regional Cancer Centre > Thiruvananthapuram > Kerala, India 695 011 >